Veterinary Services. UPDATE: USDA Influenza A Virus Surveillance Program in Swine
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1 Veterinary Services UPDATE: USDA Influenza A Virus Surveillance Program in Swine Barb Porter-Spalding, DVM MVPH Swine Health Epidemiologist U.S. Department of Agriculture Animal and Plant Health Inspection Service Veterinary Services Monday, October 26
2 Data Disclaimers: 1. Surveillance is voluntary, passive, and for the most part anonymous 2. No measure of disease prevalence by time location subtype 3. State-level data summaries are not disclosed externally beyond internal state stakeholders 2
3 Update: 1. Regional reports 2. Program analysis/review 3. Budget 4. Program efficiencies 5. Data National/Regional Phylogenetic analysis 3
4 Regional IAV-S reports for Industry: 1. Report development and content: 2014 USAHA with NPB, NPPC, and AASV 2015 AASV meeting with AASV Influenza committee Mock-up review 2. AASV Influenza Committee 3. FY 2015 Industry IAV-S reports (status) 1 st, 2 nd, and 3 rd quarter reports completed and undergoing clearance requirements before distribution 4 th quarter report data in by end of November for report development Planned distribution via posting to a USDA website and to NPB, NPPC, and AASV for sharing 4
5 5 Regional breakdown
6 Program analysis: 1. Request from NPPC for IAV-S program review/analysis to determine program value 2. Approved by APHIS administrator 3. Internal analysis - APHIS PPD, Program Assessment & Analysis group Achievements and likely outcomes generated Collect / analyze program, cooperator and key stakeholder views on current and desired future of IAV-S surveillance in the U.S. Identify / analyze IAV-S surveillance cost factors & develop forward projections 6
7 Program analysis: 4. External analysis Technical epidemiologic review Overall surveillance design, sampling efficiency, sample selection and submission process, sampled populations, representativeness of data Recommendations for process improvement and system efficiencies 5. With stakeholder collaboration will consider program revisions based on analyses results / budget 7
8 Budget: 1. Initial funding through Health and Human Services (HHS) during ph1n1 outbreak No year funding (use until money is spent) 2. Funds expected to expire in FY 2016 Once funds expended, absorbed under APHIS appropriated funding at some level FY 2015 spending above expectations, working on adjustments to conserve funding (more later) 8
9 Program efficiencies: Efficiencies implemented in June 2014 Goal - increase # of virus isolates from samples tested Evaluation: CEAH-NSU analysis of samples submitted and resulting isolates Presented and approved by the NAHLN technical working group, implemented June 2014 Efficiency: CT cutoff values established for further program testing CT < 35 for Nasal swabs and Lung; CT < 30 for OF Limit the number of Oral Fluid samples to 5 per accession ( total of 10 samples allowed per accession) Reminder of ways for novel findings to be included in the program 9
10 Impact: June 2014 program modifications: #VI's Attempted Number of VI positive samples Number of samples sequenced and sent to GenBank Comparing data from 11 months prior to the change with data from 11 months after the change, the # VI Attempted decreased, but average percent of successful VI s increased by 13.00% 10
11 Program efficiencies: Efficiencies implemented in Feb 2015 Situation: NVSL immediately propagates all viruses that are shipped to the repository and stores until requested Goal: Refine use of resources Efficiency: NVSL influenza virus propagation of : Viruses that are going into full genomic sequencing (16 viruses per month selected by NVSL based on multiple characteristics) Viruses identified by research, academic, or public health partners upon request. Impact: potential delay (2-4 weeks) in getting a virus that is not already grown out 11
12 Program efficiencies: Efficiencies under discussion: Situation: Increase in NAHLN testing in 2015 Goal: Judicious use of funds while continuing to meet program objectives and stakeholder needs Evaluation: Input received from diagnostic laboratories CEAH-SDA analysis of impact from reduction in CT cutoff values Presented to the NAHLN Technical Working Group in early July - No concerns voiced 12
13 Program efficiencies: Proposed efficiencies: Reminder: Only accessions meeting program case definition of pigs exhibiting ILI Limit 10 samples/accession, no more than 5 OF samples / accession Suggestions proposed by diagnostic laboratories: Implement a more targeted approach to sample selection Adjustments in testing algorithm New CT cutoff values for further testing Lung/Nasal CT < 30; OF CT <25 For future consideration: discontinuation of the Matrix gene sequencing The pandemic Matrix gene is the only Matrix gene found since Jan, 2015 NVSL can continue to monitor the Matrix gene through monthly WGS 13
14 14 Phylogenetic Analysis The Pay-off Continuing cooperative agreements with Dr. Amy Vincent and her lab at ARS-NADC Phylogenetic analysis of Genbank sequences from USDA IAV-S surveillance data Testing novel influenza viruses in swine Same caveats apply regarding representativeness of sample set Regional phylogenic work highlighted in regional reports Some of the phylogenic analysis information that is provided in reports data will be shared in this presentation
15 Regional breakdown 15 DATA
16 USDA IAV-S Surveillance National Program Isolation and Characterization Activities Oct July 2015 Accessions Positive Accessions ,559 Samples (not Graphed) 24,040 Accessions 8,748 Positive Accessions 2,898 Accessions with viral isolates 5,537 Accessions subtyped Subtyped Accessions Linear (Accessions) VI Positive Accessions
17 USDA IAV-S Surveillance Regional Program Isolation and Characterization Activities Oct July 2015 Swine tested Accessions Positive accessions Accessions with viral isolates Accessions subtyped Region % 8.97% 5.04% 16.69% 11.92% Region % 57.04% 52.07% 59.05% 52.63% Region % 5.45% 2.52% 8.84% 7.07% Region % 20.53% 32.10% 12.06% 20.60% Region % 0.99% 0.48% 0.42% 0.66% Unknown 5.91% 7.02% 7.80% 2.95% 7.13% 17
18 Regional breakdown of accessions in FY 2015 YTD ~7% of accessions submitted to USDA did not have a state location associated with them ~1% of accessions come from Region 5 State Provided No State recorded 18
19 USDA IAV-S Surveillance National Subtypes by Year FY 2010 FY 2015 Q H1N1 H1N H3N2 H3N1 Mixed FY 2010 FY 2011 FY 2012 FY 2013 FY 2014 FY 2015 YTD
20 USDA IAV-S Surveillance National Subtypes by Month FY2011 FY2015 Q3 250 Mixed 200 H3N1 H3N2 150 H1N2 H1N
21 Virus Type by Region Region1 Region2 Region3 Region4 Region Q4 14Q1 14Q2 14Q3 14Q4 15Q1 15Q2 15Q3 13Q4 14Q1 14Q2 14Q3 14Q4 15Q1 15Q2 15Q3 13Q4 14Q1 14Q2 14Q3 14Q4 15Q1 15Q2 15Q3 13Q4 14Q1 14Q2 14Q3 14Q4 15Q1 15Q2 15Q3 13Q4 14Q1 14Q2 14Q3 14Q4 15Q1 Number of swine isolates 15Q2 15Q3 Regional Subtypes deposited in Genbank (2 year Window) 21 H1N1 H1N2 H3N1 H3N2 mixed
22 Regional breakdown of submitted subtypes FY 2015 Q3 Percentage of Positive Accessions 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 6% 5% 3% 5% 1% 8% 28% 32% 30% 25% 44% 36% 38% 24% 27% 44% 18% 33% 42% 29% 58% 17% 46% Mixed H3N1 H3N2 H1N2 H1N1 22 0% Region 1 (n = 412) Region 2 (n = 1604) Region 3 (n = 144) Region 4 (n = 707) Region 5 (n = 12) Region Unknown (n = 116)
23 H1 phylo cluster by Region Region1 Region2 Region3 Region4 Region5 Number of swine isolates 13Q4 14Q1 14Q2 14Q3 14Q4 15Q1 15Q2 15Q3 13Q4 14Q1 14Q2 14Q3 14Q4 15Q1 15Q2 15Q3 13Q4 14Q1 14Q2 14Q3 14Q4 15Q1 15Q2 15Q3 13Q4 14Q1 14Q2 14Q3 14Q4 15Q1 15Q2 15Q3 13Q4 14Q1 14Q2 14Q3 14Q4 15Q1 15Q2 15Q3 23 alpha beta delta1 delta2 gamma pandemic
24 H3 phylo cluster by Region Region1 Region2 Region3 Region4 Region5 Number of swine isolates 13Q4 14Q1 14Q2 14Q3 14Q4 15Q1 15Q2 15Q3 13Q4 14Q1 14Q2 14Q3 14Q4 15Q1 15Q2 15Q3 13Q4 14Q1 14Q2 14Q3 14Q4 15Q1 15Q2 15Q3 13Q4 14Q1 14Q2 14Q3 14Q4 15Q1 15Q2 15Q3 13Q4 14Q1 14Q2 14Q3 14Q4 15Q1 15Q2 15Q3 24 Human_H3 IV IV A IV B IV C IV D IV E IV F
25 Region 1 FY 2015 Q3 Percentage of HA and NA combinations H3.IV A H1.pandemic percent 40 HA type H1.gamma H1.delta H1.delta1 25 N1.Classical N1.Pandemic N N NA type Total HA & NA combinations 299
26 Region 2 FY 2015 Q3 H3.IV F Percentage of HA and NA combinations H3.IV E H3.IV D H3.IV C HA type H3.IV B H3.IV A H3.IV H3.Human_H3 H1.pandemic H1.gamma percent H1.delta2 H1.delta1 H1.beta H1.alpha 26 N1.Classical N1.Pandemic N N NA type Total HA & NA combinations 857
27 H3.IV B Region 3 FY 2015 Q3 Percentage of HA and NA combinations H3.IV A HA type H3.IV H3.Human_H3 H1.pandemic H1.gamma H1.delta2 percent H1.delta1 H1.beta 27 N1.Classical N1.Pandemic N N NA type Total HA & NA combinations 87
28 H3.IV F Region 4 FY 2015 Q3 Percentage of HA and NA combinations H3.IV D H3.IV B H3.IV A percent HA type H1.pandemic H1.gamma H1.delta H1.delta1 H1.beta H1.alpha N1.Classical N1.Pandemic N N NA type 28 Total HA & NA combinations 187
29 Region 5 FY 2015 Q3 Percentage of HA and NA combinations H3.IV A HA type H1.delta1 percent N1.Classical N NA type Total HA & NA combinations 2
30 Summary: Influenza A in swine continues to be dynamic/ unstable Genomic analysis of collected data continues Minor modifications have been made to improve efficiencies in the program Working to provide regional reporting of IAV-S data to all stakeholders The USDA IAV-S Surveillance Program is currently undergoing an internal and external analysis to help direct the future of the program 30
31 Thanks to the USDA IAV-S Team USDA-STAS Beth Lautner CEAH Celia Antognoli Sara Ahola Marta Remmenga Linde Bischak John Korslund (DHS) NVSL-NAHLN Sarah Tomlinson Christie Loiacono Beth Harris Tari Moody NVSL Bev Schmitt Sabrina Swenson Alicia Janas-Martinsdale USDA-SPRS TJ Myers Swine Program Staff Lee Ann Thomas Ellen Kasari John Schiltz OHCC Joe Annelli Jane Rooney Tom Gomez ARS-NADC Marcus Kehrli Amy Vincent Rasna Walia 31
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